Towards a new Sequence Logo Visualization

sequence-logo

 

Diverging somewhat from our normal posts is a post about a new visualization developed in our group.

Eamonn is at EuroVis 2014 in Swansea this week where he will be presenting a paper viewable here Redesigning the Sequence Logo with Glyph-based Approaches to Aid Interpretation on the redesign of the infamous Sequence Logo, some screenshots which you can see below. It supports:

  1.  multiple sequence groups for comparison;
  2. entropy or frequency based encoding of bar size;
  3. glyphs to show changes in position preference for hydropathy or charge;
  4. GestaltLine glyph to show overview of variation at a position; and
  5. Customisation to:
    1. reduce transparency of positions where variability is high; or
    2. show the consensus sequence.
Screen Shot 2014-05-14 at 11.48.11

Sequence logo with entropy encoding.

 

Screen Shot 2014-05-14 at 11.49.17

Sequence logo with frequency based encoding and showing detail on demand view on position hover.

 

Everything, as always, is open source and available with examples on our GitHub repository https://github.com/ISA-tools/SequenceLogoVis. Let us know what you think, what should be improved, etc. via our issue tracker. The paper is available here and the presentation will be online soon!

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